We exploit diverse light-matter interactions and algorithms to measure architecture and dynamics of molecules, organelles, cells, organoids, and tissues. These computational microscopy platforms enable data driven discovery of biological mechanisms and therapeutic opportunities in collaboration with Chan Zuckerberg Biohub’s initiatives, platforms, and partners. Our interdisciplinary research spans fields of optics, image analytics, and biophysics. 

We pursue technological advances in following areas:

  • Label-free microscopy using phase and polarization of light.
  • Measurement of nanoscale order of molecules in 3D.
  • Developing inverse algorithms and deep learning models for converting voxels into measurements.
Our current collaborative biological research is in following areas:
  • Analyzing lifecycle and biogenesis of viruses in mammalian cells to discover new therapeutic opportunities.
  • Mapping dynamics of diverse organelles in live cells.
  • Analyzing connectivity, cell types, and myelination in brain tissue.


  • 08/02/19: Shalin presents invited talk at the Braingineers retreat of UCSC-UCSF
  • 06/10/19: Li-Hao Yeh joins the lab as R&D Engineer.
  • 06/10/19: Andrew Chen, UC Berkeley joins the lab for summer internship.
  • 06/03/19: Medha Somayaji, UC Berkeley joins us for summer internship, in collaboration with Abigail Buchwalter, UCSF.
  • 06/03/19: Lienna Chan joins us for summer internship, in collaboration with Amy Kistler, Infectious Disease, CZ Biohub.
  • 05/12/19: Shalin and Syuan-Ming teach at Deep Learning @ Marine Biological Laboratory workshop.
  • 05/09/19: The lab's first preprint is posted on bioRxiv.
  • 05/02/19: Shalin teaches phase and polarization microscopy at AQLM 2019
  • 11/27/18: Shalin presents invited talk at Optics Within Life Sciences, Australia
  • 11/22/18: Shalin presents invited talk at Institute of Molecular and Cell Biology, Singapore
  • 10/29/18: Ivan Ivanov joins the lab as R&D Engineer.
  • 10/17/18: Shalin gives invited talk at SCIEN colloquia, Stanford. 
  • 08/31/18: Bryant Chhun joins the lab as full-time R&D Engineer.
  • 08/16/18: Shalin gives invited talk at the Molecular Foundry User Meeting 2018.
  • 07/10/18: Jaehee Park joins the lab for internship.
  • 06/11/18: Bryant Chhun joins as Contract R&D Engineer.
  • 05/21/18:  Andrew Chen joins the lab for summer internship.
  • 05/03/18: Shalin to teach label-free microscopy at AQLM 2018, Woods Hole.
  • 03/29/18: Shalin gives talk at Focus on Microscopy 2018, Singapore.
  • 03/24/18: Welcoming Syuan-Ming Guo to the lab.
  • 03/24/18: Shalin gives invited talk at Center for Biomedical OCT Research, Massachusetts General Hospital.
  • 02/23/18: Shalin gives Oxyopia talk at Berkeley Vision Science. 
  • 01/23/18: Shalin gives invited talk at AIM 2018.
  • 11/30/17: Welcoming Elliot Mount to the lab.
  • 10/30/17: We are recruiting! Develop microscopes, assays, and algorithms to measure physical properties of biological systems with us!